Smart UV Unwrap on Joined Object Breaks Textures
Here what's should help. As I understand you want to bake textures.


Join objects into one.
Duplicate object and move to different layer. Name it "bake".
Remove all materials from "bake" object. Create new material for it. 
(image tex > Diffuse > output).
Create new map for baking (in UV editor) and save it as "Bake_diff"
UV unwrap "bake" obj with smart UV unwrap.
Select "Bake_diff" in image texture node as active one.
Set background on full white.
Go to Bake setup. Tick 'Selected to Active' and setup 'Ray Distance' to 0.100 
Now select both layers, select first obj with textures and as second, the bake one. (make sure image texture nod with "Bake_diff" is selected)
Bake and wait.
Save map F3


There's a blend. Prepared, just do 9 &amp; 10.